Backbone N-Amination Promotes the Folding of β-Hairpin Peptides via a Network of Hydrogen Bonds

Molecular dynamics (MD) simulations have been used to characterize the effects of backbone N-amination of residues in a model β-hairpin peptide. This modification is of considerable interest as N-aminated peptides have been shown to inhibit amyloid-type aggregation. Six derivatives of the β-hairpin peptide, which contain one, two, or four N-aminated residues, have been studied. For each peptide 100 ns MD simulations starting from the folded β-hairpin structure were performed. The effects of the N-amination prove to be very sequence dependent. N-Amination of a residue involved in interstrand hydrogen bonding (Val3) leads to unfolding of the β-hairpin, whereas N-amination of a residue toward the C-terminus (Leu11) gives fraying at the termini of the peptide. In the other derivatives the peptide remains folded, with increasing levels of N-amination reducing the right-handed twist of the β-hairpin and favoring population of a type II′ rather than a type I′ β-turn. MD simulations (100 ns) have also been run for each peptide starting from an unfolded extended chain. Here, the peptide with four N-aminated residues shows the most folding into the β-hairpin (34%). Analysis of the simulations shows that N-amination favors the population of β (φ, ψ) conformations by the preceding residue due to, at least in part, a network of weak NH2(i)–CO(i) and NH2(i)–CO(i–2) hydrogen bonds. It also leads to a reduction of misfolding because of changes in the hydrogen-bonding potential. Both of these features help funnel the peptide to the folded β-hairpin structure. The conformational insights provided through this work give a firm foundation for the design of N-aminated peptide inhibitors for modulating protein–protein interactions and aggregation.


NLEU Building Block
The hydrogen bonds were identified using the definition for medium-strong hydrogen bonds: H-acceptor distance < 0.25 nm and donor-H-acceptor angle > 135°. Populations < 5% are excluded.

Populations of clusters and of the respective hydrogen bonds (%).
The clustering was performed with a cut-off RMSD of 0.1 nm for the backbone atoms of residues 2-11.
The hydrogen bonds were identified using the definition for medium-strong hydrogen bonds: H-acceptor distance < 0.25 nm and donor-H-acceptor angle > 135°. Populations < 5% are excluded.  Table S19.

Combined clustering of the PepF and PepE trajectories. Populations of clusters and of the respective hydrogen bonds (%).
The clustering was performed with a cut-off RMSD of 0.1 nm for the backbone atoms of residues 2-11.
The hydrogen bonds were identified using the definition for medium-strong hydrogen bonds: H-acceptor distance < 0.25 nm and donor-H-Acceptor angle > 135°. Populations < 5% are excluded.

Populations of clusters and of the respective hydrogen bonds (%).
The clustering was performed with a cut-off RMSD of 0.1 nm for the backbone atoms of residues 2-11.
The hydrogen bonds were identified using the definition for medium-strong hydrogen bonds: H-acceptor distance < 0.25 nm and donor-H-Acceptor angle > 135°. Populations < 5% are excluded.

Table S21. Clustering of the PepE_N9_N11 trajectory. Populations of clusters and of the respective hydrogen bonds (%).
The clustering was performed with a cut-off RMSD of 0.1 nm for the backbone atoms of residues 2-11.
The hydrogen bonds were identified using the definition for medium-strong hydrogen bonds: H-acceptor distance < 0.25 nm and donor-H-acceptor angle > 135°. Populations < 5% are excluded.

Populations of clusters and of the respective hydrogen bonds (%).
The clustering was performed with a cut-off RMSD of 0.1 nm for the backbone atoms of residues 2-11.
The hydrogen bonds were identified using the definition for medium-strong hydrogen bonds: H-acceptor distance < 0.25 nm and donor-H-acceptor angle > 135°. Populations < 5% are excluded.  The clustering was performed with a cut-off RMSD of 0.1 nm for the backbone atoms of residues 2-11.
The hydrogen bonds were identified using the definition for medium-strong hydrogen bonds: H-acceptor distance < 0.25 nm and donor-H-Acceptor angle > 135°. Populations < 5% are excluded. The clustering was performed with a cut-off RMSD of 0.1 nm for the backbone atoms of residues 2-11.
The hydrogen bonds were identified using the definition for medium-strong hydrogen bonds: H-acceptor distance < 0.25 nm and donor-H-Acceptor angle > 135°. Populations < 5% are excluded. * The highest hydrogen bond population from the donor NZ-HZ1, NZ-HZ2 or NZ-HZS3 is listed Table S25. Combined clustering of the PepF_N2_N4_N9_N11 and PepE_N2_N4_N9_N11 trajectories. Populations of clusters and of the respective hydrogen bonds (%).
The clustering was performed with a cut-off RMSD of 0.1 nm for the backbone atoms of residues 2-11.
The hydrogen bonds were identified using the definition for medium-strong hydrogen bonds: H-acceptor distance < 0.25 nm and donor-H-acceptor angle > 135°. Populations < 5% are excluded.